So the air is appearing on the suction side of the pump?? Are the tank vents free enough to allow air to replace consumed fuel? Are you using an orbit type clunk in any of the tanks? I had one in my fueling jug (completely submerged) and presumeably it would not let fuel flow as fast as the pump wanted it, and it created a big stream of bubbles. Once discovered, I cut the screen off the clunk and problem solved (Although I have one less level of filtering now...)

BTW I had to completely drain my fuel system last fall when transporting my F-16 by air.. when we fueled up, there were (not unexpectedly) huge bubbles passing completely through the pump into the MW-54.. It took about 5 minutes of shaking and bouncing in all attitudes to purge the UAT. During the whole exercise, the little Wren kept running - the bubbles didn't seem to bother it at all!!!
( and no, I would not knowingly fly it with bubbles in the system!!)